Currently, the UCSF Mass Spectrometry Facility is equipped with two PerSeptive Biosystems Voyager and one AutoSpec MALDI instruments. Optimization of methods of sample preparation and laser configuration would enable the most efficient and productive use of the available instruments. Sensitivity enhancement would improve the data quality for researchers. Comparison of the two Voyager instruments has established equivalent sensitivity for both in linear and reflectron modes using standard dried droplet matrix preparation on a cze standard with chca matrix. The minimum requirement for detection with this method is from 10 to 100 fmol. To improve upon these limits, a protocol involving nitrocullulose/chca mixtures is being tested and has been demonstrated to allow detection at low fmol levels, with reproducibility in question at lower levels. Increased laser focus has been tested without improvement, but needs to be tested in conjunctuion with the nitrocullulose/chca sample preparation techniques. Usefulness for lab samples such as in gel digests will be evaluated once clear improvements on standards have been demonstrated. A second area of development is the use of alternative matrices and comparison of the UV and IR laser for MALDI. IR laser in conjunction with suitable matrices has been shown to reduce metastable decay of sialated and phosphorylated peptides. However, difficulties with laser stability and sample crystallization impede widespread use of the technique. Thus, development of appropriate sample preparation methods and optimal laser settings on the Voyager DE-STR IR system will be continued. Samples currently of interest to the group will take priority, such as sulfated peptides.